PhD Chapter 1

Campaign 2014 - Maps and exploration

This series of files compile analyses done for the specific analysis of Chapter 1, for the local campaign of 2014.

All analyses have been done with PRIMER-e 6 and R 4.0.4.

Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it

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We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

Abundances of Bipalponephtys neotena (Bneo) and Spisula solidissima (Ssol) were also considered (see IndVal and SIMPER results).

Statistics for each variable considered:

  Mean SD SE Median Min Max 95% CI
om 2.265 1.630 0.364 2.016 0.278 8.260 0.714
gravel 0.000 0.000 0.000 0.000 0.000 0.000 0.000
sand 0.050 0.224 0.050 0.000 0.000 1.000 0.098
silt 0.001 0.000 0.000 0.001 0.000 0.001 0.000
clay 0.949 0.223 0.050 0.999 0.000 1.000 0.098
arsenic 3.345 1.424 0.319 3.150 1.100 6.000 0.624
cadmium 0.131 0.040 0.009 0.135 0.040 0.190 0.018
chromium 72.875 25.652 5.736 75.850 31.700 143.300 11.242
copper 17.640 6.952 1.555 18.850 3.300 32.400 3.047
iron 69456.658 31948.948 7144.002 64356.210 32899.910 188857.220 14001.986
manganese 1934.067 1243.717 278.104 1475.005 705.690 5962.190 545.073
mercury 0.029 0.058 0.013 0.015 0.000 0.250 0.025
lead 6.278 2.988 0.668 6.240 1.020 12.180 1.310
zinc 70.030 22.198 4.964 71.550 15.900 101.500 9.728
S 25.250 6.463 1.445 27.000 10.000 34.000 2.833
N 1140.150 665.407 148.790 1322.500 36.000 2103.000 291.622
H 1.866 0.338 0.075 1.882 1.246 2.737 0.148
J 0.590 0.121 0.027 0.585 0.409 0.929 0.053
  Mean SD SE Median Min Max 95% CI
om 0.471 0.238 0.053 0.385 0.187 0.877 0.104
gravel 0.034 0.106 0.024 0.007 0.000 0.481 0.046
sand 0.247 0.439 0.098 0.000 0.000 1.000 0.192
silt 0.008 0.007 0.001 0.008 0.000 0.022 0.003
clay 0.711 0.433 0.097 0.968 0.000 0.993 0.190
arsenic 2.095 0.633 0.142 1.950 1.400 3.700 0.277
cadmium 0.101 0.045 0.010 0.090 0.030 0.220 0.020
chromium 58.165 32.082 7.174 53.400 10.900 125.000 14.060
copper 4.450 3.818 0.854 3.250 2.200 19.400 1.673
iron 58989.194 31326.220 7004.756 55172.005 14089.920 146603.720 13729.069
manganese 890.020 383.078 85.659 927.960 251.670 1638.110 167.888
mercury 0.000 0.000 0.000 0.000 0.000 0.000 0.000
lead 2.337 0.836 0.187 2.225 1.090 4.960 0.367
zinc 36.295 8.823 1.973 36.150 18.400 55.300 3.867
S 15.700 6.208 1.388 16.000 6.000 35.000 2.721
N 141.800 219.010 48.972 64.000 14.000 941.000 95.984
H 1.813 0.479 0.107 1.953 0.911 2.457 0.210
J 0.681 0.175 0.039 0.678 0.315 0.938 0.077

1. Maps

1.1. General map

1.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Species

Richness

Density

Diversity

Evenness

2. Figures

2.1. Barplots

Organic matter

Grain-size

Heavy metals

Species abundances

Diversity indices

2.2. Phylum frequencies

Conditions
Phylum abundances by condition
Phylum HI R
Annelida 20360 1135
Phoronida 1138 2
Arthropoda 883 749
Mollusca 361 743
Cnidaria 42 40
Bryozoa 8 22
Platyhelminthes 5 0
Echinodermata 4 139
Hemichordata 2 0
Chaetognatha 0 1
Nematoda 0 0
Nemertea 0 5
Sipuncula 0 0

Sites
Phylum abundances by site
Phylum P1 P2 P3 P4 R1 R2 R3 R4
Annelida 6065 7459 6155 681 43 106 926 60
Phoronida 408 317 412 1 0 0 1 1
Arthropoda 289 317 219 58 40 281 399 29
Mollusca 60 113 80 108 30 381 110 222
Cnidaria 13 11 9 9 11 15 7 7
Bryozoa 4 1 0 3 0 14 2 6
Echinodermata 4 0 0 0 20 65 49 5
Platyhelminthes 1 0 4 0 0 0 0 0
Chaetognatha 0 0 0 0 0 1 0 0
Hemichordata 0 0 2 0 0 0 0 0
Nematoda 0 0 0 0 0 0 0 0
Nemertea 0 0 0 0 0 5 0 0
Sipuncula 0 0 0 0 0 0 0 0

2.3. Species estimation curves

2.4. Principal Component Analysis

Parameters + Metals

Variables have been standardized by mean and standard-deviation.

Parameters

Variables have been standardized by mean and standard-deviation.

Metals

Variables have been standardized by mean and standard-deviation.

2.5. Non-metric Multidimensional Scaling

Parameters + Metals

Variables have been standardized by mean and standard-deviation.

Parameters

Variables have been standardized by mean and standard-deviation.

Metals

Variables have been standardized by mean and standard-deviation.

Species

Stations with no species were deleted from this analysis.

2.6. Hierarchical Agglomerative Clustering

Parameters + Metals

Variables have been standardized by mean and standard-deviation.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  1  1  3  1  3  3  3  3  3  2  3  3  3  2 
## 31 32 33 34 35 36 37 38 39 40 
##  2  3  2  3  2  3  3  3  3  3

Parameters

Variables have been standardized by mean and standard-deviation.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  1  1  1  1  3  3  3  3  3  2  3  3  3  2 
## 31 32 33 34 35 36 37 38 39 40 
##  2  3  2  3  2  3  3  3  3  3

Metals

Variables have been standardized by mean and standard-deviation.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 
##  1  2  1  1  1  1  2  1  1  1  2  3  2  2  2  3  3  2  2  2  2  2  2  3  2  3  3  3  3  3 
## 31 32 33 34 35 36 37 38 39 40 
##  3  3  3  3  3  2  2  3  3  3

Species

Stations with no species were deleted from this analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  2  2  2  1  2  2  2  2  2  2  2  2  2  2 
## 31 32 33 34 35 36 37 38 39 40 
##  2  2  2  2  2  2  2  2  2  2

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